After the Fact
by BTM707
Summary: After the destruction of the BSL and the X Parasite, Samus laments the changes in her life, and how the galaxy will never again be the same.


_So this is basically a collection of thoughts that popped into my head out of nowhere. I mean seriously, I wasn't even playing a Metroid game or anything. It was just "BOOP - hey, this would be good for a story!" For those who are wondering, "This isn't Complement or Change of Heart, so why are you doing something different?" ...I dunno. I am just one confusing asshole, I guess. At any rate, this takes place shortly after Metroid Fusion, and basically revolves around the premise that it's chronologically the last game in the series to date. So if another game is ever released after Fusion... Well, then this was three hours down the tube. I hope you can enjoy it though! That said, enjoy!_

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**After the Fact**

Leaning back into her seat as the laboratory behind her exploded with the planet in a brilliant light, Samus let a sigh of relief escape her lips. It was over – the BSL station was destroyed, along with any trace of the Metroids' repopulation. There was no chance that anyone would be able to harness their existence as a weapon, nor was there an opportunity for them to roam free beyond any semblance of control. She had, for the umpteenth time, rescued the galaxy from the possibility of domination or destruction. So, as she flew away from the burning remains of her mission, ever further into the vast expanse of stars that stretched before her view, why did she not feel at peace?

Typically after a mission of this scale, she'd be exhausted. With little rest to be had throughout the process of its completion, she could spend almost an entire day afterward in a deep, dreamless slumber, compensating for the bursts of adrenaline she was frequented to experiencing. Indeed, she had been unconscious for almost a month after her last mission to Zebes, though that was understandably a different kind of fatigue; the strain on her body after the acquisition and usage of that powerful weapon, combined with the emotional turmoil she'd experienced throughout that entire ordeal with Mother Brain, had rendered her in a near coma for weeks when she had finally escaped the planet's destruction and given in to her body's exhaustion. While she felt that she could certainly sleep for a fortnight right now, a concern lurked in the shadows of her mind, its persistent nagging preventing her from what should have been a well-deserved rest.

Rising from her seat, Samus slowly peeled off her helmet. It was because everything had changed, she realized with another sigh. Not in an immediate sense, but over the last few months, or even years, events had transpired to change her view of what she thought she knew, and what her role in everything truly was. She had been raised by her people to become a guardian, a savior against the forces that threatened to upset the balance of life. In the beginning, that enemy had clearly been the Space Pirate organization and their quest for power. She knew their ways intimately, of course, being one of a very few number of survivors throughout their ruthless raids. She'd tangled with them countless times, and personally dealt their operations quite a bit of damage. She had even taken down the supreme Mother Brain on two separate occasions, and even _that_ could be chalked up to three times if that included the incident with MB – or 'Melissa', though identifying the android as a person still left her feeling uncomfortable. And even that didn't hold a candle to her long-standing rivalry with her parents' killer. Despite their numerous struggles and her frequent victories, Ridley managed to plague her with his existence even after his death on Zebes – reappearing before her eyes not once, but twice. _Only that miserable bastard can haunt me after I leave his corpse to blow up with a planet._

But the Pirate threat had – she thought – been completely and truly eradicated after the destruction of Zebes and their calculating leader. But this mission, as well as her last one, had her questioning the identity of her true foe. Yes, the Bottle Ship Incident had been an unmitigated disaster under the direction of a few corrupt officials within the Galactic Federation's ranks, but the Biologic Space Laboratories station had been a publically supported project under the direct authority of the Galactic Federation High Council. It was one thing for a few selfish people to be dabbling in Pirate history and Metroids; it was quite another for the leaders of the galactic republic to be doing the same.

The Galactic Federation had been an organization she'd spent her life aligned with. If she was not fighting _with_ them, she was at least fighting _for _them – and for what they represented. But the incident with the Bottle Ship had, for the first time in her life, shaken her trust in the institute and its goals. It was true that the High Council claimed no responsibility or even knowledge of the bioweapon project's existence, but the thought of traitors within the Federation still scared her. But this – _it was almost a repeat of the Bottle Ship_, she thought with a frown. She had uncovered a similar plan to utilize the Metroids' abilities, only this time representatives of the Federation had _tried_ to keep the truth from her. There was no way the High Council could feign innocence this time; to push the idea of the research station only to claim ignorant of its true purpose would not even fool a child. They could argue they kept the information from her in order to protect her from what they'd consider 'unsettling news', given her past with the creatures, but they could not back up illegal cloning of the galaxy's most dangerous subject. If the truth of the matter got out, there would be unified chaos everywhere she looked.

But it wouldn't, and she knew it. Her actions to subdue the imminent threat had defied direct orders from the High Council, and there would be a reprimanding. Even ignoring the fact that she had destroyed a multi-billion dollar research facility – as well as yet _another_ planet, never mind one the Federation was actively studying – she could be court-martialled for insubordination. Or she could if she was still in the army; now she wouldn't be surprised if they tried to find a way to throw her in prison for life. Or argue to have her executed. Either way, her future with the Federation looked rather bleak at best. There was a pretty good chance she'd have a substantial bounty on her head because of her actions. She might have to spend the rest of her life on the run.

With a fleeting mental command, her suit dispersed, leaving her in the Zero Suit she often donned under her armour. Rubbing a hand over her tired eyes, she fought back a shiver as a chill sent itself down her spine. _Of course_, she thought bitterly as she bit her lip in frustration. It wasn't just her situation that had changed: now that she carried Metroid DNA within her, she was more susceptible to cold. Naturally, reacquiring her Varia upgrade had negated the issue on the station, but it did little to protect her outside of the suit. But of course, the problem ran as deep as her very genetic makeup; there _was_ little she could do about it.

Adjusting the cabin's temperature, she examined herself in a powerless monitor. Her exhausted features stared back through her piercing blue eyes – or eye, rather. She blinked in surprise, studying her own gaze carefully. Her left eye was normal, the deep oceanic blue with just a touch of green that she knew so well. But her right eye had become much lighter, taking on more of a green quality as opposed to her natural blue. Her contrasting gaze had her thinking back years ago, when her struggle with her dark reflection had reached a galactic-level conflict. Throughout those missions the corruptive Phazon had ravaged her body more and more, until her physical features and genetic coding had been unrecognizable to her own ship. Her eyes had changed then, as well: they had become brighter and scarier, augmented by the dark blue veins that sprouted from her sockets and crawled along her face. She had almost become a monster, a fact that she recalled with a shudder. Why, then, was her eye changing now? Another side-effect of the Metroid vaccine? And why green? Because it was the colour of the Metroids' membrane? If that _was_ the case, it would at least be preferable to matching their blood-red nuclei. Even so, though, she hardly needed yet another physical reminder about how much had changed. Why didn't she just drag a knife across her face so that fate wouldn't be able to scar that for her too?

Taking a deep breath, she tried to calm her thoughts. She wasn't quite sure why a colour-change would bother her – after all, she spent a lot of her time behind her visor anyway, so there were few who would even know about it. The thought of her visor, however, had the brief moment of comfort flitting away. Her suit, her entire _existence_, had been changed as well. Gone was her familiar armour, with a sheen that sent chills down her foes, and the large round shoulders that offered her vulnerable neck some degree of safety. In its place was a thin membrane-like suit that, while much more flexible, did not offer near the level of protection as its predecessor. At the very least she had managed to restore its colour to the familiar orange and yellow, rather than that bright blue or that _gaudy_ green and pink. Even so, it was little comfort to what she had lost. _It's not enough to have an eye match a Metroid, or to share a weakness with a Metroid_ _– no, my entire suit has to resemble a bloody Metroid, too. _Why did fate have to be so cruel? She was becoming more and more like the very creatures she despised.

…With the notable exception, of course. She sank back into her chair and placed her face in her hand, leaning on the armrest for support. That little baby Metroid, the innocent creature that had mistakenly imprinted on her as its mother, had managed to save her life twice. The poor thing had simply hatched at the wrong time, caught in a struggle between her and the Pirates. In its short life it had been taken to be studied by researchers, kidnapped by the Pirates, extensively cloned, and then killed while trying to save her from Mother Brain. And then, when she stupidly let herself get infected by the X Parasite, the infant's DNA had managed to bring her back from the brink of death. It was ironic, she supposed, that the DNA within her came from the very last Metroid in the galaxy – the one she had been ordered to destroy, and the one that ultimately gave its life for her. Just as she had begun to feel a sort of attachment for the creature, it too had been taken from her; it seemed that the Pirates could not let her have anything as long as they existed. She felt no remorse at all for their extermination.

At least she had learned to cope with the baby Metroid's passing. But the Federation seemed bent on reminding her of its existence with a myriad of cloning schemes. Of course, the Federation never played fair; they were all about maintaining power, rather than swaying to it. How many times in the past had she saved civilian lives during her missions, or even coming to the rescue of Federation officials? But did they keep score? She snorted to herself. _The minute they save my life, they draw up a new contract because I'm now 'their property'. Good to know my past deeds mean nothing to them_. In a way, she wasn't sorry for defying the Council's orders. Not just because they had little respect for the future of all life, but because they had no respect for their history with her. She had done more fighting the Pirates than they could've ever hoped to, but it ultimately meant nothing to them. But that's the way they were. Back when she was younger and an active soldier in the Federation Army, she used to angrily think that the High Council cared more about being a business than maintaining a galactic republic. That the memory would return to her now almost brought a small smirk to her face.

But that was just the way they were. They saw societal lifeforms as nothing more than numbers. How they could have even conceived that cloning Metroids could be a good idea was beyond her; hadn't they heard enough of her tales to know the risk the creatures posed? Was that not why their extermination had been ordered in the first place? She shook her head. It scared her to think that the Pirates' operations and the Bottle Ship Incident had put ideas in their heads. The Metroids were too dangerous to be used as weapons – why could no one see that? Well, surely _some_ of them had – she knew for a fact that scientists who had studied Metroids as far back as the Phazon Chronicles were wary of their destructive capabilities. Military personnel who had faced Metroids in combat were knowledgeable about the threat as well; she knew of a number of highly respected generals who shared her concerns with the lifeforms. But the scientists and generals on the Council would have been overruled by the majority – the _politicians_, the ones who cared more for public opinion than public safety. She ground her teeth together in anger, forming a fist so tight that her knuckles popped. Those people would be the death of society as they knew it if they kept this up. And she couldn't even fight them directly about it – not if they took the destruction of their station badly, and she knew they would.

She sighed, letting her eyes trace over the unfamiliar control panel of her ship. That's right – she'd lost her ship, too, the only place she'd ever considered a home. Of course the Federation had provided her with a new one, but only at the cost of doing their orders in eliminating the threat. Or was she just 'studying' the X for them? Was the parasite to be used as a weapon as well? She shook her head slowly. The High Council's short-sightedness was beyond comprehension. All they cared about was money and power. Not the risk they took playing with biological weapons, not the threat of destruction toward society, and especially not towards everything _she_ had lost in the process of their acquisition. If there was _one_ positive to come out of this entire mess, it was that she was reunited with one of the few friends she had, one that she thought she'd lost forever.

Reaching back, she drew her elastic from her ponytail, allowing her hair to cascade over her shoulders. After Old Bird and the rest of the Chozo had vanished from her life, Adam was the closest thing to a father she'd had. Though she'd hated admitting it at the time, he'd taught her much when she was a soldier: not so much in combat skills, where she'd already surpassed him, but regarding interpersonal skills, which she'd been sorely lacking in after initially leaving Zebes and joining the army. Being torn from him during the Bottle Ship Incident had cut her deeply – especially after she was just starting to repair things between them. That she would manage to find him again, and on her side, no less, was nothing short of a miracle. Heaven knows she'd need an ally throughout what was to come.

She'd had no knowledge of the Federation's habit of 'resurrection'. While the idea was intriguing, the morality of it still shook her. Did Adam get a say in his rebirth? Was there a chance he did not want to exist as computer data? He was just a mind now, robbed of a body – unless the ship itself counted, but the thought of that simply seemed too bizarre for her. And how much of Adam was still him, anyway? In the beginning he'd clearly been under the influence of some sort of programming, purposefully keeping secrets from her. While he'd eventually come to side with her, she knew that the real Adam would never have agreed with the Metroid Breeding Project. Was it truly Adam that was in her computer? Did he still have a consciousness? He _had_ chosen to help her and disobey his programming, so perhaps he did. Perhaps that programming had been a sort of prison for him, something to hinder his thoughts. She had to believe it was really him. After all, her former CO had asked for her trust in the past; she had certainly learned enough by now to know when to give it.

Staring out the viewport, she allowed her vision to blur over the racing stars. Adam had been oddly quiet since their departure; he must've been occupied with something. She was content to leave him to his dealings and get some rest, but the concern continued to prevent her from doing so. Until she knew the Federation's stance on her actions, she had nowhere to go. Would the High Council recognize the danger she'd helped them avoid, or would they brand her a traitor? If the latter was the case, she wouldn't be able to get half a parsec near a civilized world without being hunted. Her career would be over, and her life would basically be forfeit. But if the Federation tried something new that she deemed corrupt, and there was no one to oppose them…

She closed her eyes and leaned her head back into her seat, gently massaging the bridge of her nose. In no life would she have thought the Galactic Federation might become her foe. She _had _defeated one of the largest forces in the galaxy, but she'd had the backing of the Federation to do it. The Federation itself, however, managed thousands of worlds in the galaxy; there was no realistic way she could take them on directly. The problem was the corruption that had quite obviously infiltrated their ranks. There were individual people in the organization that had the power to influence entire worlds; the thought that any of them might abuse that power was terrifying. There had to be a way to alert _someone_ to the actions of the High Council. Surely the entirety of the Federation's politicians could collectively overrule their decrees. Her brow knit in frustration. There had to be something she could do.

"Samus."

Her eyes flicked open and slowly trailed over to the control panel where a light had pinged, signalling Adam's active state. She let a sigh escape her lips before she answered. "What is it?"

"I have been analyzing the data regarding the Metroid Breeding Project, as well as that of the Federation High Council's involvement. We have to discuss what it is we need to do from here on out."

"As interesting as that sounds, I would prefer to get some sleep before we talk about whatever comes next." As she spoke she struggled to fight back a yawn. The fatigue was definitely starting to get to her.

"I'm afraid that is not an option at the moment. We have work to do."

She raised a brow at the computer's inflection. "Does that mean you have a plan?"

"The beginnings of one. But we must act now before the Council deems you a threat to the galaxy. As doubtful as such an accusation is, I believe there is a good chance of it occurring."

Her future was unclear, that much was certain. If she was branded a traitor, would the people who knew her, people like Anthony, believe the lies? Certainly not: Anthony knew her well enough to know she wouldn't act against orders unless it was truly necessary. Even so, she had to prevent the opportunity from surfacing. Straightening in her seat, she activated the ship's manual steering controls and grabbed the wheel. Fighting back the exhaustion, she settled into a comfortable position and focused on the tasks that needed to be done. "I suppose we'd better get to it then."

It was true that everything had changed; the more she thought back on the last few years, the more she realized that statement was valid. But if her new foe was to be the Galactic Federation, then so be it: whether it was directly or confidentially, she would fight her hardest to keep the people throughout the galaxy safe. For that was who she was, that which the Chozo raised her to be: a galactic saviour, the one who would battle the evils that threatened the existence of life as they knew it. If she had to fight to her last breath to keep the very organization she'd aligned with from obtaining galactic dominance, then that was what she would do. Because she was Samus Aran, the warrior among the stars, the Chozo's prophesized saviour, and the galaxy's last hope. She would always fight. And she would not stop until she had succeeded.

But as she took off into the infinite reaches of space, she could not help the wave of sadness that washed over her, nor the frown that tugged at her lips. Because while she had always known she would need to become the galaxy's greatest hero, she had never imagined just how much she'd have to sacrifice in order to achieve peace.


End file.
